Degenerate primers - (May/24/2005 )

i was reading an article in which the primer sequences had alphabets like Y and R in them.
Can anyone explain why these Y and R are in the sequence?

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http://hcgs.unh.edu/protocol/basic/pcrdegenpri.html

Degenerate primers are useful for pulling out one part of a gene sequence when you only know the gene sequence in related organisms. The more distant those related organsims, the more difficult it can be to design primers.

One solution is to gather sequences from a large range of organisms (say all vertebrates if you are working on fishes), translate them to amino acid sequence and align them. Based on these alignments, you can identify regions of the sequence which are highly conserved at the amino acid level. These conserved regions become possible locations for degenerate primers.

Degenerate primers are designed to match an amino acid sequence. A DNA sequence and its corresponding amino acid sequence would be

P F T K
CCn TTy ACn AAr

n = A,C,G or T
y = C,T
r = A,G

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